>TIGR00348 hsdR type I site-specific deoxyribonuclease, HsdR family; InterPro: IPR004473 There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements , , as summarised below: Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA. Type I restriction endonucleases are components of prokaryotic DNA restriction-modification mechanisms that protects the organism against invading foreign DNA. Type I enzymes have three different subunits subunits - M (modification), S (specificity) and R (restriction) - that form multifunctional enzymes with restriction (3.1.21.3 from EC), methylase (2.1.1.72 from EC) and ATPase activities , . The S subunit is required for both restriction and modification and is responsible for recognition of the DNA sequence specific for the system. The M subunit is necessary for modification, and the R subunit is required for restriction. These enzymes use S-Adenosyl-L-methionine (AdoMet) as the methyl group donor in the methylation reaction, and have a requirement for ATP. They recognize asymmetric DNA sequences split into two domains of specific sequence, one 3-4 bp long and another 4-5 bp long, separated by a nonspecific spacer 6-8 bp in length. Cleavage occurs a considerable distance from the recognition sites, rarely less than 400 bp away and up to 7000 bp away. Adenosyl residues are methylated, one on each strand of the recognition sequence. These enzymes are widespread in eubacteria and archaea. In enteric bacteria they have been subdivide into four families: types IA, IB, IC and ID. This entry represents the R subunit (HsdR) of type I restriction endonucleases such as EcoRI (3.1.21.3 from EC), which recognises the DNA sequence 5'-GAATTC; the R protein (HsdR) is required for both nuclease and ATPase activity , , , .; GO: 0003677 DNA binding, 0005524 ATP binding, 0009035 Type I site-specific deoxyribonuclease activity, 0009307 DNA restriction-modification system.

Probab=99.59  E-value=4.5e-15  Score=105.74  Aligned_cols=162  Identities=18%  Similarity=0.226  Sum_probs=92.7

Q ss_pred             CHHHHHHHHHHHH-----------CCCCEEEECCCCCHHHHHHHHHHHHH---HCCCCCEEEEECCCCCHHHHHHHHHHH
Q ss_conf             4899999999996-----------79819996899988999999999997---408994899723310137889999851
Q gi|254780129|r    6 KPHQIVMVNWLLS-----------HDRCALWASMGSGKTVSVLFALSTIK---ILDPRPVLIIAPLRVAQYVWKDEVERW   71 (220)
Q Consensus         6 rp~Q~~a~~~~~~-----------~~~~~l~~~~G~GKT~~ai~~~~~~~---~~~~~~~LIi~P~s~~~~~W~~e~~~~   71 (220)
T Consensus       299 ~y~qy~av~ki~~~~~~~~~~k~~~n~G~iWHtQGSGKtlTm~f~A~k~~~~~~~~~p~v~fvvDR~eLd~Ql~~~~~~~  378 (813)
T TIGR00348       299 RYMQYRAVKKIVESILRKEKGKDKRNKGLIWHTQGSGKTLTMLFLARKLRKQKELKNPKVFFVVDRRELDEQLYKEFSSL  378 (813)
T ss_pred             HHHHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEECCCHHHHHHHHHHHHHHHHHHCCCEEEEEEECHHHHHHHHHHHHHH
T ss_conf             88999999999999985313788636744898507637889999999998746526984999972727788999999876


Q ss_pred             CCCCCCEEEEEECCCCC---CCCCC--------CCCCCEEEECHHHHHC----CCCCCCCCCCC-------C-CCCCCHH
Q ss_conf             55346069986112101---12234--------5676627865667310----00000002472-------0-0002512
Q gi|254780129|r   72 SAFSDMTVSSLIGSERQ---RIKAL--------NTPAHLYIINFENIPW----LVKMKLDHWDF-------A-TIVVDES  128 (220)
Q Consensus        72 ~~~~~~~~~~~~~~~~~---~~~~~--------~~~~~~~i~~~~~l~~----~~~~~~~~~~~-------~-~iIiDEa  128 (220)
T Consensus       379 ~~~~~~~~~~~e-S~~~Lk~~L~~~~~sennPn~~k~g~~~t~IqKF~~~~~~k~~e~~~~~~~~i~~~r~~vv~i~DEa  457 (813)
T TIGR00348       379 KDLIKDCAERIE-SIAELKELLEKNDESENNPNISKRGIIITTIQKFDDELLDKLKEEEEKFPESIIIDRKEVVVIIDEA  457 (813)
T ss_pred             HHHCHHHHHCCC-CHHHHHHHHHHCCCCCCCCCCCCCCEEEEEEECCCHHHHHHHHHHHHCCCCEEEEEECCEEEEEECC
T ss_conf             420101042067-8889999875177645675535676799960010403445368887438736898716089997067


Q ss_pred             HCCCCCC------CCCHHHHHHHHHHHHHCCCCEEEEECCCCCCCCHH
Q ss_conf             2013654------33203699999998513798799831653248889
Q gi|254780129|r  129 TKLKSFR------THQGTKQTRALGKVAFSKVKRFIELTGTPSPNGLI  170 (220)
Q Consensus       129 H~~kn~~------~~~~~k~~k~l~~~~~~~~~~~l~LTgTPi~n~~~  170 (220)
T Consensus       458 HRsqyG~tqklhnGkfqtGla~~~~~~l--knA~f~gFTGTPI~~~d~  503 (813)
T TIGR00348       458 HRSQYGKTQKLHNGKFQTGLAKALKKAL--KNASFFGFTGTPISKKDR  503 (813)
T ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHHHC--HHHHHHCCCCCCCCHHCC
T ss_conf             5553534110004413589999998743--112010122477653247